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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:gep2pep.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings gep2pep_1.31.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/gep2pep.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gep2pep/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gep2pep’ version ‘1.31.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘gep2pep’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
checkRd: (-1) as.CategorizedCollection.Rd:27: Lost braces; missing escapes or markup?
    27 |     in the collection to {CategorizedCollection}. If
       |                          ^
checkRd: (-1) gep2pep-package.Rd:50-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gep2pep-package.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gep2pep-package.Rd:55-56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gep2pep-package.Rd:58-61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gep2pep-package.Rd:63-65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gep2pep-package.Rd:67-69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gep2pep-package.Rd:71-73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) loadESmatrix.Rd:19: Lost braces
    19 |     reports the ES for the pathway \code{i}, condition{j}. If
       |                                                       ^
checkRd: (-1) loadPVmatrix.Rd:19: Lost braces
    19 |     reports the PV for the pathway \code{i}, condition{j}. If
       |                                                       ^
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • empty test (1): 'test_rawMode.R:216:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_gep2pep.R:148:5'): KS statistics ─────────────────────────────
  Expected `ksSGE$ES` to equal `loadESmatrix(rp, "SGE")[g, s]`.
  Differences:
  1/1 mismatches
  [1] 0.5 - -0.5 == 1
  
  [ FAIL 1 | WARN 2271 | SKIP 1 | PASS 153 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/gep2pep.Rcheck/00check.log’
for details.

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###
### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL gep2pep
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library’
* installing *source* package ‘gep2pep’ ...
** this is package ‘gep2pep’ version ‘1.31.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (gep2pep)

R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(gep2pep)
> 
> test_check("gep2pep")
Saving _problems/test_gep2pep-148.R
Chunk 1 of 2, 523 bytes (current file size: 4.3 Kb)
Chunk 2 of 2, 671 bytes (current file size: 16.3 Kb)
Chunk 1 of 2, 542 bytes (current file size: 4.3 Kb)
Chunk 2 of 2, 703 bytes (current file size: 16.3 Kb)
Chunk 1 of 2, 553 bytes (current file size: 4.3 Kb)
Chunk 2 of 2, 694 bytes (current file size: 16.3 Kb)
[ FAIL 1 | WARN 2271 | SKIP 1 | PASS 153 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test_rawMode.R:216:1'

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_gep2pep.R:148:5'): KS statistics ─────────────────────────────
Expected `ksSGE$ES` to equal `loadESmatrix(rp, "SGE")[g, s]`.
Differences:
1/1 mismatches
[1] 0.5 - -0.5 == 1

[ FAIL 1 | WARN 2271 | SKIP 1 | PASS 153 ]
Error:
! Test failures.
Execution halted